R Observatory: Metrics for MetaProViz version 4.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MetaProViz

Bioc current

METabolomics pre-PRocessing, functiOnal analysis and VIZualisation

v4.0.0 · software · BSD_3_clause + file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.23 · Apr 29, 2026

Current · Requires R 4.6

1.0 In 1 of 49 releases 3.23

Description

MetaProViz can analyse standard metabolomics and exometabolomics data (CoRe). It performs pre-processing including feature filtering, missing value imputation, normalisation and outlier detection. It performs functional analysis including differential metabolite analysis (DMA), clustering based on regulatory rules (MCA) and contains different visualisation methods to extract biological interpretable graphs and saves them in a publication ready format.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

127 38 exported

Complexity

9.3 avg / 60 max

Call network

127 nodes / 228 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

31,094

Files

145

Compiled share

0%

Has compiled src

No

Language breakdown

R 23,675 (76.1%)Tests 94 (0.3%)Docs 3,051 (9.8%)Vignettes 4,274 (13.7%)

API

Exported functions

39

Internal functions

86

Recent export changes

v3.23+39 %>%, checkmatch_pk_to_data, cluster_ora +36 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

3

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

97.4%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

6

Dep constraint coverage

7.3%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.4

System requirements

–

C++ standard

–

License

BSD_3_clause + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

1

First release

2026-04-28

Latest release

2026-04-28

Avg cadence

–

Cold removal rate

–

Dep drift

0

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 802 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 89%
Return-value docs: 100%
References docs: 0%

Topics

Software › StatisticalMethod › Clustering

Software › ResearchField › Metabolomics

Software › WorkflowStep › Pathways

Software › WorkflowStep › QualityControl

Software

Software › ResearchField › SystemsBiology

Software › WorkflowStep › Visualization

People

Christina Schmidt author maintainer fnd
Macabe Daley author
Jannik Franken author
Christian Frezza author
Dimitrios Prymidis author
Julio Saez-Rodriguez author
Denes Turei author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MetaProViz")

Format

Schmidt, C., Daley, M., Franken, J., Frezza, C., Prymidis, D., Saez-Rodriguez, J., & Turei, D. (2026). MetaProViz: METabolomics pre-PRocessing, functiOnal analysis and VIZualisation (Version 4.0.0) [Computer software]. https://bioconductor.org/packages/MetaProViz

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for MetaProViz version 4.0.0 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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